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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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do_refine option in SatsumaSynteny2 #3

Closed hughesdj closed 7 years ago

hughesdj commented 8 years ago

Running SatsumaSynteny2 with the do_refine option set gives an error, because shell cannot find HomologyByXCorr. @grabherr Should the shell call HomologyByXCorrSlave as it does earlier?

Command: $prog_path"SatsumaSynteny2" -t $target -q $query -o out2 -do_refine 1 -slaves 8 -threads 8

Output tail: .. Merging XCorr matches: /home/apps/rothhpc1-cluster/src/satsuma2/satsuma2-master/bin/MergeXCorrMatches -i out2/xcorr_aligns.final.out -q /home/data/hughesdj/Duplication/satsuma/Svim_scaffs.fa -t /home/data/hughesdj/Duplication/satsuma/Spur_19Chrs.fa -o out2/satsuma_summary.chained.out > out2/MergeXCorrMatches.chained.out == Processing finished, waiting for the slaves to die == TIME SPENT WORKING: 15551 == Processing finished, waiting for the slaves to die == TIME SPENT WORKING: 15552 Running refined matches (fill in the blanks): /home/apps/rothhpc1-cluster/src/satsuma2/satsuma2-master/bin/HomologyByXCorr -cutoff 1.2 -q /home/data/hughesdj/Duplication/satsuma/Svim_scaffs.fa -t /home/data/hughesdj/Duplication/satsuma/Spur_19Chrs.fa -o out2/xcorr_aligns.refined.out -guide out2/xcorr_aligns.final.out > out2/HomologyByXCorr.refined.out sh: /home/apps/rothhpc1-cluster/src/satsuma2/satsuma2-master/bin/HomologyByXCorr: No such file or directory Merging XCorr matches: /home/apps/rothhpc1-cluster/src/satsuma2/satsuma2-master/bin/MergeXCorrMatches -i out2/xcorr_aligns.refined.out -q /home/data/hughesdj/Duplication/satsuma/Svim_scaffs.fa -t /home/data/hughesdj/Duplication/satsuma/Spur_19Chrs.fa -o out2/satsuma_summary.refined.out > out2/MergeXCorrMatches.refined.out terminate called after throwing an instance of 'CMException' sh: line 1: 68774 Aborted /home/apps/rothhpc1-cluster/src/satsuma2/satsuma2-master/bin/MergeXCorrMatches -i out2/xcorr_aligns.refined.out -q /home/data/hughesdj/Duplication/satsuma/Svim_scaffs.fa -t /home/data/hughesdj/Duplication/satsuma/Spur_19Chrs.fa -o out2/satsuma_summary.refined.out > out2/MergeXCorrMatches.refined.out Joining Workqueue thread SATSUMA: all done, date and time: 2016/08/11 18:48:02

bjclavijo commented 7 years ago

HomologyByXCorr should have been built. It seems there's a bunch of missing binaries there. We'll have a look.

jonwright99 commented 7 years ago

@hughesdj can you tell me which binaries you have in /home/apps/rothhpc1-cluster/src/satsuma2/satsuma2-master/bin/. Compiling should create the following;

BlockDisplaySatsuma ChainMatches Chromosemble ChromosomePaint ColaAlignSatsuma FilterGridSeeds HomologyByXCorrSlave KMatch MatchDump MatchesByFeature MergeScaffoldsBySynteny MergeXCorrMatches MicroSyntenyPlot OrderOrientBySynteny ReverseSatsumaOut satsuma_run.sh SatsumaSynteny2 SatsumaToFASTA SatsumaToGFF SortSatsuma

jonwright99 commented 7 years ago

and now I see that HomologyByXCorr isn't compiled. Sorry, being a bit slow today. I'll patch this.

hughesdj commented 7 years ago

@jonwright99 Thanks, yes all the binaries listed above are present, but not HomologyByXCorr, which shell calls when do_refine option is set. Were you able to fix? Is issue closed?

jonwright99 commented 7 years ago

Hi David, We've fixed this now. If you pull the latest code you should see HomologyByXCorr is now compiled into the bin directory and the do_refine option works. Sorry for the delay in fixing this.